Posted by
Jirka on
Jun 27, 2014; 5:04pm
URL: http://imagej.273.s1.nabble.com/Image-Stitching-problem-tp5008473.html
Good morning
I have com difficulty with the ImageJ Stitching Plugins. I used it some
time ago without any problem, I made a macro for several image series,
which now does not work. Well I need to merge together row of 9 images so I
used following command (I used the same images and the same configuration
as I had used 2 years ago and it worked fine):
run("Grid/Collection stitching", "type=[Grid: snake by rows] order=[Right &
Down ] grid_size_x=9 grid_size_y=1 tile_overlap=5
first_file_index_i=0
directory=/home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif
file_names=29-041-Izd2-Cc10-5-les1_p{ii}.tif
output_textfile_name=TileConfiguration-test.txt fusion_method=[Linear
Blending] regression_threshold=0.30 max/avg_displacement_threshold=2.50
absolute_displacement_threshold=3.50 subpixel_accuracy
computation_parameters=[Save memory (but be slower)] image_output=[Fuse and
display]");
But in the end it pastes 9 times the first image in row by size of 9
consecutive frames and the log is following:
Stitching internal version: 1.1
Loading (0, 0):
/home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p00.tif
...
2080x1540px, channels=3, timepoints=1 (899 ms)
Loading (1, 0):
/home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p01.tif
...
2080x1540px, channels=3, timepoints=1 (893 ms)
Loading (2, 0):
/home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p02.tif
...
2080x1540px, channels=3, timepoints=1 (905 ms)
Loading (3, 0):
/home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p03.tif
...
2080x1540px, channels=3, timepoints=1 (876 ms)
Loading (4, 0):
/home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p04.tif
...
2080x1540px, channels=3, timepoints=1 (903 ms)
Loading (5, 0):
/home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p05.tif
...
2080x1540px, channels=3, timepoints=1 (863 ms)
Loading (6, 0):
/home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p06.tif
...
2080x1540px, channels=3, timepoints=1 (890 ms)
Loading (7, 0):
/home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p07.tif
...
2080x1540px, channels=3, timepoints=1 (894 ms)
Loading (8, 0):
/home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p08.tif
...
2080x1540px, channels=3, timepoints=1 (876 ms)
29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
0.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
1976.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
3952.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
5928.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
7904.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
9880.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
11856.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
13832.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
15808.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
Fuse & Display ...
Finished fusion (4777 ms)
Finished ... (12785 ms)
It seems to find fine transformation but I think that the problem is that
it pastes always Tile #1. What am I doing wrong or is there a bug?
Thanks
--
Best regards, Jiri Borovec
----------------------------------------------------------------------------------------------------
Jiří Borovec <jiri.borovec@fel.cvut.cz>
PhD student at CMP CTU, ISC member
http://cmp.felk.cvut.cz/~borovji3--
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